Linkage disequilibrium

Water buffalo genome characterization by the Illumina BovineHD BeadChip

R. R. A. Borquis, Baldi, F., de Camargo, G. M. F., Cardoso, D. F., Santos, D. J. A., Lugo, N. H., Sargolzaei, M., Schenkel, F. S., Albuquerque, L. G., and Tonhati, H., “Water buffalo genome characterization by the Illumina BovineHD BeadChip”, vol. 13, pp. 4202-4215, 2014.

To define the best strategies for genomic association studies and genomic selection, it is necessary to determine the extent of linkage disequilibrium (LD) and the genetic structure of the study population. The current study evaluated the transference of genomic information contained in the Illumina BovineHD BeadChip from cattle to buffaloes, and assessed the extent of the LD in buffaloes.

Analysis of the haplotype and linkage disequilibrium of PPARγ gene polymorphisms rs3856806, rs12490265, rs1797912, and rs1175543 among patients with metabolic syndrome in Kazakh of Xinjiang Province

S. X. Guo, Guo, H., Ma, R. L., Ding, Y. S., Zhang, J. Y., Liu, J. M., Zhang, M., Niu, Q., Qiang, N., Li, S. G., and Qi, C. N., “Analysis of the haplotype and linkage disequilibrium of PPARγ gene polymorphisms rs3856806, rs12490265, rs1797912, and rs1175543 among patients with metabolic syndrome in Kazakh of Xinjiang Province”, vol. 13, pp. 8686-8694, 2014.

We investigated the relationship between haplotype and linkage disequilibrium of the PPARγ gene polymorphisms rs3856806, rs12490265, rs1797912, and rs1175543 and metabolic syndrome (MS) in the Kazakh people of Xinjiang Province. For PPARγ, rs3856806, rs12490265, rs1797912, and rs1175543 genotypes were detected in 489 subjects (including 245 MS patients and 244 controls) using matrix-assisted laser desorption-ionization time-of-flight mass spectrometry.

Significance of linkage disequilibrium heterogeneous patterns in the 21q22.3 region for mapping 21 trisomy individuals

Y. Valle, Padilla-Gutiérrez, J. R., Quintero-Ramos, A., García-González, I. J., and Rivas, F., “Significance of linkage disequilibrium heterogeneous patterns in the 21q22.3 region for mapping 21 trisomy individuals”, vol. 12. pp. 2821-2828, 2013.

Recombination patterns can be indirectly inferred by means of linkage disequilibrium (LD) estimates, since LD is negatively correlated with genetic distance. However, LD does not necessarily have absolute correspondence with genetic distance. We estimated LD at 5 loci located in the 21q22.3 region. These STRs (D21S1440, D21S168, D21S1260, D21S1446, and D21S1411) covered 8.81 Mb of the 21q22.3 region. They were genotyped by conventional PCR. Similar size samples previously validated by sequencing were used as a genotyping control.

Differences in frequencies of UGT1A9, 1A7, and 1A1 genetic polymorphisms in Chinese Tibetan versus Han Chinese populations

W. Yan, Wang, Y. W., Yang, F. F., Wang, M., Zhang, X. Q., Dong, J., Chen, E., and Yang, J., “Differences in frequencies of UGT1A9, 1A7, and 1A1 genetic polymorphisms in Chinese Tibetan versus Han Chinese populations”, vol. 12, pp. 6454-6461, 2013.

As part of a series of pharmacogenomics studies of the Chinese population, we investigated genetic polymorphisms of some UGT1A regions. The three genes that were analyzed were UGT1A9, 1A7, and 1A1; we sequenced their exons, together with promoters, surrounding introns and 3'-untranslated regions (3ꞌUTR) in 100 unrelated-healthy Chinese Tibetan individuals. We compared the data with information on Han Chinese of the same region, which we downloaded from the HapMap database. We identified 40 polymorphisms; 16 of them were shared by the two populations.

Association of single nucleotide polymorphisms with carcass traits in Nellore cattle

J. B. S. Ferraz, Pinto, L. F. B., Meirelles, F. V., Eler, J. P., de Rezende, F. M., Oliveira, E. C. M., Almeida, H. B., Woodward, B., and Nkrumah, D., “Association of single nucleotide polymorphisms with carcass traits in Nellore cattle”, vol. 8, pp. 1360-1366, 2009.

The association between two single nucleotide polymorphisms (SNPs), T945M and UCP1SNP1, with hot carcass weight (HCW, kg, N = 618), longissimus dorsi muscle area (REA, cm2, N = 633), and backfat thickness (BF, mm, N = 625), measured in Nellore cattle in Brazil, was evaluated. Likelihood ratio tests were used to evaluate reduced (fixed effects of general mean, contemporary group, yearling weight, age at slaughter, and random effect of infinitesimal genetic value) and full model (reduced model effects plus quantitative trait locus effects).

Identification and characterization of polymorphisms at the HSA α1-acid glycoprotein (ORM*) gene locus in Caucasians

C. M. Owczarek, Owczarek, A. L., and Board, P. G., “Identification and characterization of polymorphisms at the HSA α1-acid glycoprotein (ORM*) gene locus in Caucasians”, vol. 1, pp. 96-105, 2002.

Human α1-acid glycoprotein (AGP) or orosomucoid (ORM) is a major acute phase protein that is thought to play a crucial role in maintaining homeostasis. Human AGP is the product of a cluster of at least two adjacent genes located on HSA chromosome 9. Using a range of restriction endonucleases we have investigated DNA variation at the locus encoding the AGP genes in a group of healthy Caucasians. Polymorphisms were identified using BamHI, EcoRI, BglII, PvuII, HindIII, TaqI and MspI.

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